If you want to get into deep tax policy, then I think that 501(c)(3)s should have to produce yearly reports that detail how money was spent. Some charities that use paid promoters and solicitors end up handing over as much as 80% (or more, in some extreme cases) of their profits to the for-profit groups. Those charities should lose their status, because essentially the government is losing tax revenue to employ people to harass families when they eat (and because charities are not considered commercial speech, the Do Not Call Registry doesn't apply to them). Of course, I managed to get all of them to stop calling me years ago by starting to ask them what percentage of their revenue went to the charity itself and what was spent on promotion, advertising and third party services. I noticed that they started hanging up on me and the calls stopped altogether a year later.

The point is that, in principle, I think that churches should be considered charities. Scientology, however, is clearly not a charity, but a tax dodge masquerading as a religion for the purpose of abusing the existing 501(c)(3) regulations and no-action letters. Of course, even then, they were able to defend their 501(c)(3) status, as I'm sure you're aware. I think that a re-write of the Code that gave the IRS the means to challenge Scientology again would probably result in a quick disbanding of that quack religion, especially now that their power base has imploded.

As for your last question, "What about religions that do more harm than good?", I think that it's a subjective question in most cases where the activity isn't blatantly criminal (and therefore not tax-exempt anyway). A Southern Evangelical would say that Islam and Judaism do more harm than good, insofar as they lack Christ and, lacking Christ, they lead their followers away from God. An atheist might say all religions do more harm than good because they reinforce quaint and anachronistic notions of the metaphysical makeup of the universe and impose a "big old guy in the sky" with arbitrary rules on a society that has advanced beyond that point.